Starting phenix.real_space_refine
on Thu Mar 13 21:20:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vfx_31962/03_2025/7vfx_31962.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vfx_31962/03_2025/7vfx_31962.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vfx_31962/03_2025/7vfx_31962.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vfx_31962/03_2025/7vfx_31962.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vfx_31962/03_2025/7vfx_31962.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vfx_31962/03_2025/7vfx_31962.cif"
  }
  resolution = 2.8
  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=   0.004
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      64      5.16       5
     C    5781      2.51       5
     N    1512      2.21       5
     O    1647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9004
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2323
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 12, 'TRANS': 282}
    Chain: "A"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1756
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 38
          Classifications: {'peptide': 4}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 102
          Unusual residues: {'CLR': 3, 'PLM': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 5.86, per 1000 atoms: 0.65
  Number of scatterers: 9004
  At special positions: 0
  Unit cell: (90.1, 124.95, 123.25, 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      64     16.00
     O    1647      8.00
     N    1512      7.00
     C    5781      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  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: 2.49
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      38.9% alpha, 24.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'R' and resid 22 through 54
      removed outlier: 3.610A  pdb=" N   ASP R  26 " --> pdb=" O   TYR R  22 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 76
    Processing helix  chain 'R' and resid 77 through 87
      removed outlier: 3.853A  pdb=" N   PHE R  81 " --> pdb=" O   THR R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 137
    Processing helix  chain 'R' and resid 138 through 146
    Processing helix  chain 'R' and resid 146 through 163
      removed outlier: 4.459A  pdb=" N   TRP R 150 " --> pdb=" O   ILE R 146 " (cutoff:3.500A)
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 186 through 209
      removed outlier: 3.825A  pdb=" N   ARG R 190 " --> pdb=" O   ASP R 186 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   ASN R 192 " --> pdb=" O   LYS R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 231
    Processing helix  chain 'R' and resid 236 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 273
      removed outlier: 4.193A  pdb=" N   GLN R 273 " --> pdb=" O   ARG R 269 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 303
      removed outlier: 4.218A  pdb=" N   ALA R 288 " --> pdb=" O   ASP R 284 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU R 289 " --> pdb=" O   VAL R 285 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASN R 293 " --> pdb=" O   LEU R 289 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   SER R 294 " --> pdb=" O   ALA R 290 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   CYS R 295 " --> pdb=" O   PHE R 291 " (cutoff:3.500A)
      Proline residue:  R 298  - end of helix
    Processing helix  chain 'R' and resid 305 through 315
    Processing helix  chain 'A' and resid 8 through 31
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 4.000A  pdb=" N   ARG A 205 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.811A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.537A  pdb=" N   GLU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.552A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.612A  pdb=" N   ALA A 299 " --> pdb=" O   THR A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 351
      removed outlier: 4.181A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 10 through 24
      removed outlier: 3.693A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.890A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 164 through 169
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 5.990A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.179A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.906A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.894A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.957A  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: 6.738A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.112A  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: 6.956A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.155A  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: 6.499A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.727A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.536A  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: 6.126A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.498A  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: 6.126A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 4.353A  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
    Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195
      removed outlier: 6.607A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)

    458 hydrogen bonds defined for protein.
    1287 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: 2.93

  Time building geometry restraints manager: 2.93 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: 2864
        1.34 -     1.46: 2238
        1.46 -     1.58: 4003
        1.58 -     1.70: 0
        1.70 -     1.82: 95
  Bond restraints: 9200
  Sorted by residual:
  bond pdb=" SD  FME C   1 "
       pdb=" CE  FME C   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.750  0.055 2.00e-02 2.50e+03 7.58e+00
  bond pdb=" CG  FME C   1 "
       pdb=" SD  FME C   1 "
    ideal  model  delta    sigma   weight residual
    1.817  1.771  0.046 2.00e-02 2.50e+03 5.35e+00
  bond pdb=" N   FME C   1 "
       pdb=" CN  FME C   1 "
    ideal  model  delta    sigma   weight residual
    1.335  1.374 -0.039 2.00e-02 2.50e+03 3.88e+00
  bond pdb=" CA  GLN B  75 "
       pdb=" C   GLN B  75 "
    ideal  model  delta    sigma   weight residual
    1.522  1.490  0.032 1.72e-02 3.38e+03 3.45e+00
  bond pdb=" C10 CLR R 402 "
       pdb=" C9  CLR R 402 "
    ideal  model  delta    sigma   weight residual
    1.551  1.517  0.034 2.00e-02 2.50e+03 2.91e+00
  ... (remaining 9195 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 12159
        1.70 -     3.39: 238
        3.39 -     5.09: 60
        5.09 -     6.78: 13
        6.78 -     8.48: 1
  Bond angle restraints: 12471
  Sorted by residual:
  angle pdb=" N   VAL S  64 "
        pdb=" CA  VAL S  64 "
        pdb=" C   VAL S  64 "
      ideal   model   delta    sigma   weight residual
     113.20  109.73    3.47 9.60e-01 1.09e+00 1.30e+01
  angle pdb=" CB  MET R 197 "
        pdb=" CG  MET R 197 "
        pdb=" SD  MET R 197 "
      ideal   model   delta    sigma   weight residual
     112.70  121.18   -8.48 3.00e+00 1.11e-01 7.98e+00
  angle pdb=" CA  VAL R 302 "
        pdb=" C   VAL R 302 "
        pdb=" N   PHE R 303 "
      ideal   model   delta    sigma   weight residual
     116.60  120.42   -3.82 1.45e+00 4.76e-01 6.94e+00
  angle pdb=" CA  CYS S  96 "
        pdb=" CB  CYS S  96 "
        pdb=" SG  CYS S  96 "
      ideal   model   delta    sigma   weight residual
     114.40  120.19   -5.79 2.30e+00 1.89e-01 6.33e+00
  angle pdb=" C   MET A 240 "
        pdb=" N   ASN A 241 "
        pdb=" CA  ASN A 241 "
      ideal   model   delta    sigma   weight residual
     121.54  126.34   -4.80 1.91e+00 2.74e-01 6.32e+00
  ... (remaining 12466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.42: 5263
       24.42 -    48.83: 275
       48.83 -    73.25: 34
       73.25 -    97.67: 12
       97.67 -   122.08: 1
  Dihedral angle restraints: 5585
    sinusoidal: 2300
      harmonic: 3285
  Sorted by residual:
  dihedral pdb=" CA  GLN B  75 "
           pdb=" C   GLN B  75 "
           pdb=" N   ASP B  76 "
           pdb=" CA  ASP B  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.85   21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  GLN S 142 "
           pdb=" C   GLN S 142 "
           pdb=" N   ALA S 143 "
           pdb=" CA  ALA S 143 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.31  -20.69     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" C10 CLR R 403 "
           pdb=" C1  CLR R 403 "
           pdb=" C2  CLR R 403 "
           pdb=" C3  CLR R 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -56.83   65.25 -122.08     1      3.00e+01 1.11e-03 1.63e+01
  ... (remaining 5582 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 992
       0.042 -    0.084: 324
       0.084 -    0.127: 94
       0.127 -    0.169: 12
       0.169 -    0.211: 7
  Chirality restraints: 1429
  Sorted by residual:
  chirality pdb=" C13 CLR R 403 "
            pdb=" C12 CLR R 403 "
            pdb=" C14 CLR R 403 "
            pdb=" C17 CLR R 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.72   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" C13 CLR R 402 "
            pdb=" C12 CLR R 402 "
            pdb=" C14 CLR R 402 "
            pdb=" C17 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.74   -0.19 2.00e-01 2.50e+01 9.50e-01
  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   -2.75   -0.19 2.00e-01 2.50e+01 8.66e-01
  ... (remaining 1426 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL S 147 "    0.062 5.00e-02 4.00e+02   9.43e-02 1.42e+01
        pdb=" N   PRO S 148 "   -0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO S 148 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO S 148 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO B 194 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU R 158 "    0.029 5.00e-02 4.00e+02   4.32e-02 2.99e+00
        pdb=" N   PRO R 159 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO R 159 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO R 159 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1355
        2.76 -     3.29: 8272
        3.29 -     3.83: 14381
        3.83 -     4.36: 17237
        4.36 -     4.90: 30477
  Nonbonded interactions: 71722
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OD2 ASP B 153 "
            pdb=" NE2 GLN B 156 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" ND2 ASN B 340 "
            pdb=" OD1 ASN G  59 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" O   GLY S 112 "
            pdb=" OG  SER S 184 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" NZ  LYS S 163 "
            pdb=" OE2 GLU S 234 "
     model   vdw
     2.336 3.120
  ... (remaining 71717 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:             0.920
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.830
  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:             0.010
  Load rotamer database and sin/cos tables:14.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9200  Z= 0.221
  Angle     :  0.654   8.477  12471  Z= 0.351
  Chirality :  0.046   0.211   1429
  Planarity :  0.004   0.094   1552
  Dihedral  : 15.033 122.082   3456
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1120
  helix:  1.62 (0.27), residues: 400
  sheet:  0.28 (0.30), residues: 287
  loop : -0.99 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.019   0.001   PHE B 199 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.005   0.000   ARG A 242 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.129 
Fit side-chains
REVERT: R   44 ASN cc_start: 0.8230 (m110) cc_final: 0.7988 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 1.9492
  time to fit residues: 246.7959
Evaluate side-chains
  100 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 87 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
R  66 ASN
R 108 ASN
S 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.133410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.090381 restraints weight = 12632.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 2.37
r_work: 0.2894 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8761
moved from start:          0.0879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   9200  Z= 0.229
  Angle     :  0.596   7.092  12471  Z= 0.315
  Chirality :  0.044   0.140   1429
  Planarity :  0.004   0.040   1552
  Dihedral  :  7.563  58.535   1436
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  6.91 %
    Favored  : 91.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.25), residues: 1120
  helix:  1.78 (0.26), residues: 402
  sheet:  0.35 (0.30), residues: 286
  loop : -0.94 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.013   0.001   TYR S 190 
 ARG   0.003   0.000   ARG B  42 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.936 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7075 (mtp180)
REVERT: A  297 GLU cc_start: 0.7890 (mp0) cc_final: 0.7673 (mp0)
REVERT: G   19 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5379 (mp)
  outliers start: 16
  outliers final: 1
  residues processed: 113
  average time/residue: 1.3586
  time to fit residues: 162.8829
Evaluate side-chains
  109 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 63 optimal weight:    0.4980
   chunk 67 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 96 optimal weight:    9.9990
   chunk 76 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 71 optimal weight:    9.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
R  66 ASN
R 108 ASN
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.134640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.091218 restraints weight = 12856.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 2.40
r_work: 0.2910 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8745
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9200  Z= 0.168
  Angle     :  0.535   7.728  12471  Z= 0.285
  Chirality :  0.042   0.136   1429
  Planarity :  0.003   0.035   1552
  Dihedral  :  6.660  59.543   1436
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.48 %
    Favored  : 89.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.25), residues: 1120
  helix:  1.85 (0.26), residues: 409
  sheet:  0.42 (0.30), residues: 291
  loop : -0.93 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.015   0.001   TYR A 287 
 ARG   0.002   0.000   ARG B 197 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 1.054 
Fit side-chains
REVERT: R   44 ASN cc_start: 0.8290 (m110) cc_final: 0.8015 (m110)
REVERT: A  287 TYR cc_start: 0.7669 (m-80) cc_final: 0.7453 (m-80)
REVERT: B  217 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6988 (pp-130)
REVERT: G   19 LEU cc_start: 0.5611 (OUTLIER) cc_final: 0.5127 (mp)
REVERT: S  234 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8175 (mt-10)
REVERT: S  245 LEU cc_start: 0.8748 (tt) cc_final: 0.8471 (tp)
  outliers start: 10
  outliers final: 2
  residues processed: 111
  average time/residue: 1.4421
  time to fit residues: 169.5551
Evaluate side-chains
  106 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 41 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.133230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.089978 restraints weight = 12711.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.31
r_work: 0.2894 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9200  Z= 0.222
  Angle     :  0.559   6.219  12471  Z= 0.299
  Chirality :  0.043   0.139   1429
  Planarity :  0.004   0.036   1552
  Dihedral  :  6.618  57.421   1436
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.24 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.25), residues: 1120
  helix:  1.85 (0.26), residues: 408
  sheet:  0.42 (0.30), residues: 293
  loop : -0.89 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.017   0.001   PHE B 199 
 TYR   0.012   0.001   TYR A 287 
 ARG   0.004   0.000   ARG G  27 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 1.079 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7068 (mtp180)
REVERT: A  287 TYR cc_start: 0.7664 (m-80) cc_final: 0.7355 (m-80)
REVERT: A  318 GLU cc_start: 0.8045 (tt0) cc_final: 0.7497 (mm-30)
REVERT: G   19 LEU cc_start: 0.5696 (OUTLIER) cc_final: 0.5180 (mp)
REVERT: G   21 MET cc_start: 0.7330 (tpp) cc_final: 0.6922 (mmp)
REVERT: S   43 LYS cc_start: 0.8480 (mptt) cc_final: 0.8206 (mppt)
REVERT: S  234 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8149 (mt-10)
REVERT: S  245 LEU cc_start: 0.8771 (tt) cc_final: 0.8514 (tp)
  outliers start: 14
  outliers final: 4
  residues processed: 106
  average time/residue: 1.2982
  time to fit residues: 146.4986
Evaluate side-chains
  107 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0770
   chunk 24 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 90 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0970
   chunk 55 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.7738

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.136817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.094318 restraints weight = 12707.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.37
r_work: 0.2956 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9200  Z= 0.126
  Angle     :  0.488   7.010  12471  Z= 0.262
  Chirality :  0.041   0.130   1429
  Planarity :  0.003   0.032   1552
  Dihedral  :  6.122  59.562   1436
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.86 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.25), residues: 1120
  helix:  2.06 (0.26), residues: 409
  sheet:  0.61 (0.30), residues: 283
  loop : -0.77 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 297 
 HIS   0.002   0.000   HIS A 188 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.005   0.000   ARG G  27 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7022 (mtp180)
REVERT: A  287 TYR cc_start: 0.7636 (m-80) cc_final: 0.7401 (m-80)
REVERT: A  311 ASN cc_start: 0.8549 (t0) cc_final: 0.8261 (t0)
REVERT: A  318 GLU cc_start: 0.8045 (tt0) cc_final: 0.7520 (mm-30)
REVERT: B  217 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7056 (pp-130)
REVERT: G   19 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.5181 (mp)
REVERT: G   38 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8156 (ttp)
REVERT: S  219 LEU cc_start: 0.8297 (tt) cc_final: 0.8079 (tt)
REVERT: S  245 LEU cc_start: 0.8752 (tt) cc_final: 0.8527 (tp)
  outliers start: 14
  outliers final: 5
  residues processed: 115
  average time/residue: 1.3215
  time to fit residues: 161.7003
Evaluate side-chains
  114 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain G residue   38 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 37 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
R 108 ASN
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.135925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.093428 restraints weight = 12618.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.34
r_work: 0.2942 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9200  Z= 0.152
  Angle     :  0.508   7.544  12471  Z= 0.271
  Chirality :  0.041   0.135   1429
  Planarity :  0.003   0.033   1552
  Dihedral  :  6.072  59.428   1436
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.68 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.25), residues: 1120
  helix:  2.07 (0.26), residues: 409
  sheet:  0.68 (0.31), residues: 274
  loop : -0.68 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.000   HIS S  35 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.004   0.000   ARG G  27 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 1.088 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7031 (mtp180)
REVERT: A  287 TYR cc_start: 0.7595 (m-80) cc_final: 0.7310 (m-80)
REVERT: A  311 ASN cc_start: 0.8569 (t0) cc_final: 0.8282 (t0)
REVERT: A  318 GLU cc_start: 0.8097 (tt0) cc_final: 0.7609 (mm-30)
REVERT: B  217 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7001 (pp-130)
REVERT: G   19 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5184 (mp)
REVERT: S  234 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8084 (mt-10)
REVERT: S  245 LEU cc_start: 0.8780 (tt) cc_final: 0.8528 (tp)
  outliers start: 19
  outliers final: 8
  residues processed: 115
  average time/residue: 1.4033
  time to fit residues: 171.9978
Evaluate side-chains
  115 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  160 VAL
Chi-restraints excluded: chain R residue  229 HIS
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0970
   chunk 82 optimal weight:    8.9990
   chunk 105 optimal weight:    0.0170
   chunk 110 optimal weight:    7.9990
   chunk 83 optimal weight:    8.9990
   chunk 109 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9980
   chunk 45 optimal weight:   10.0000
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.4816

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

Flipped N/Q/H residues before XYZ refinement:
R 293 ASN
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.138691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.095812 restraints weight = 12934.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 2.15
r_work: 0.3015 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9200  Z= 0.115
  Angle     :  0.484   9.686  12471  Z= 0.255
  Chirality :  0.040   0.128   1429
  Planarity :  0.003   0.033   1552
  Dihedral  :  5.708  59.201   1436
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.30 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.25), residues: 1120
  helix:  2.23 (0.26), residues: 409
  sheet:  0.75 (0.31), residues: 272
  loop : -0.64 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.002   0.000   HIS A 188 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.005   0.000   ARG B  42 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 1.115 
Fit side-chains
REVERT: R   44 ASN cc_start: 0.8229 (m110) cc_final: 0.7975 (m110)
REVERT: A  242 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7093 (mtp180)
REVERT: A  287 TYR cc_start: 0.7569 (m-80) cc_final: 0.7263 (m-80)
REVERT: A  311 ASN cc_start: 0.8546 (t0) cc_final: 0.8322 (t0)
REVERT: A  318 GLU cc_start: 0.8041 (tt0) cc_final: 0.7529 (mm-30)
REVERT: A  329 THR cc_start: 0.7718 (m) cc_final: 0.7466 (t)
REVERT: B   38 ASP cc_start: 0.8126 (t0) cc_final: 0.7916 (m-30)
REVERT: B  217 MET cc_start: 0.7409 (ptt) cc_final: 0.7087 (pp-130)
REVERT: G   19 LEU cc_start: 0.5615 (OUTLIER) cc_final: 0.5113 (mp)
  outliers start: 16
  outliers final: 6
  residues processed: 120
  average time/residue: 1.5909
  time to fit residues: 203.9437
Evaluate side-chains
  114 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 74 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   chunk 68 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.133828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.091910 restraints weight = 13001.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3095 rms_B_bonded: 2.27
r_work: 0.2918 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9200  Z= 0.229
  Angle     :  0.566   9.563  12471  Z= 0.299
  Chirality :  0.043   0.139   1429
  Planarity :  0.003   0.032   1552
  Dihedral  :  6.155  56.825   1436
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.12 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1120
  helix:  2.05 (0.26), residues: 410
  sheet:  0.63 (0.30), residues: 286
  loop : -0.64 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.017   0.001   PHE B 199 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.003   0.000   ARG G  27 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 1.094 
Fit side-chains
REVERT: A  242 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7069 (mtp180)
REVERT: A  287 TYR cc_start: 0.7620 (m-80) cc_final: 0.7331 (m-80)
REVERT: A  311 ASN cc_start: 0.8633 (t0) cc_final: 0.8286 (t0)
REVERT: A  318 GLU cc_start: 0.8141 (tt0) cc_final: 0.7640 (mm-30)
REVERT: A  329 THR cc_start: 0.7754 (m) cc_final: 0.7500 (t)
REVERT: B  217 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7028 (pp-130)
REVERT: G   19 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5260 (mp)
REVERT: S  245 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8495 (mp)
  outliers start: 13
  outliers final: 6
  residues processed: 117
  average time/residue: 1.3059
  time to fit residues: 162.8521
Evaluate side-chains
  115 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue   80 PHE
Chi-restraints excluded: chain S residue  245 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 108 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 99 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 84 optimal weight:   30.0000
   chunk 9 optimal weight:    0.9980
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.133971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.090471 restraints weight = 12785.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.13
r_work: 0.2917 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9200  Z= 0.223
  Angle     :  0.571   9.312  12471  Z= 0.303
  Chirality :  0.043   0.137   1429
  Planarity :  0.003   0.032   1552
  Dihedral  :  6.254  55.816   1436
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.43 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.25), residues: 1120
  helix:  1.98 (0.26), residues: 409
  sheet:  0.67 (0.30), residues: 279
  loop : -0.74 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.017   0.001   PHE R 308 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.003   0.000   ARG B  42 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.984 
Fit side-chains
REVERT: R  304 MET cc_start: 0.8107 (mmp) cc_final: 0.7889 (mmm)
REVERT: A  242 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7082 (mtp180)
REVERT: A  287 TYR cc_start: 0.7548 (m-80) cc_final: 0.7274 (m-80)
REVERT: A  318 GLU cc_start: 0.8134 (tt0) cc_final: 0.7641 (mm-30)
REVERT: A  329 THR cc_start: 0.7772 (m) cc_final: 0.7533 (t)
REVERT: B   42 ARG cc_start: 0.7632 (ttt-90) cc_final: 0.7336 (ttp80)
REVERT: B  217 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6990 (pp-130)
REVERT: G   19 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5222 (mp)
REVERT: S  234 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8070 (mt-10)
  outliers start: 16
  outliers final: 5
  residues processed: 116
  average time/residue: 1.2971
  time to fit residues: 160.4319
Evaluate side-chains
  116 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 29 optimal weight:    0.3980
   chunk 55 optimal weight:    7.9990
   chunk 76 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 66 optimal weight:    0.3980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
R 179 ASN
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.136063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.093033 restraints weight = 12870.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.32
r_work: 0.2956 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9200  Z= 0.144
  Angle     :  0.525   9.796  12471  Z= 0.277
  Chirality :  0.041   0.130   1429
  Planarity :  0.003   0.033   1552
  Dihedral  :  5.930  58.082   1436
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 15.26 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.25), residues: 1120
  helix:  2.12 (0.26), residues: 410
  sheet:  0.78 (0.31), residues: 273
  loop : -0.60 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 297 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.002   0.000   ARG G  27 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.901 
Fit side-chains
REVERT: R   44 ASN cc_start: 0.8215 (m110) cc_final: 0.7946 (m110)
REVERT: A  242 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7024 (mtp180)
REVERT: A  287 TYR cc_start: 0.7518 (m-80) cc_final: 0.7239 (m-80)
REVERT: A  311 ASN cc_start: 0.8583 (t0) cc_final: 0.8270 (t0)
REVERT: A  318 GLU cc_start: 0.8117 (tt0) cc_final: 0.7631 (mm-30)
REVERT: A  329 THR cc_start: 0.7725 (m) cc_final: 0.7477 (t)
REVERT: B  217 MET cc_start: 0.7328 (ptt) cc_final: 0.6975 (pp-130)
REVERT: G   19 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5241 (mp)
REVERT: S  234 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7979 (mt-10)
  outliers start: 10
  outliers final: 5
  residues processed: 112
  average time/residue: 1.3580
  time to fit residues: 161.7973
Evaluate side-chains
  112 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  266 VAL
Chi-restraints excluded: chain R residue  295 CYS
Chi-restraints excluded: chain A residue  242 ARG
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain G residue   19 LEU
Chi-restraints excluded: chain S residue  234 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 95 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 89 optimal weight:    6.9990
   chunk 84 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.131840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.087779 restraints weight = 12805.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.14
r_work: 0.2883 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9200  Z= 0.320
  Angle     :  0.635   9.762  12471  Z= 0.336
  Chirality :  0.045   0.147   1429
  Planarity :  0.004   0.032   1552
  Dihedral  :  6.542  55.996   1436
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.85 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.25), residues: 1120
  helix:  1.84 (0.26), residues: 410
  sheet:  0.63 (0.30), residues: 283
  loop : -0.72 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.006   0.001   HIS S  35 
 PHE   0.020   0.002   PHE A 189 
 TYR   0.013   0.002   TYR A 320 
 ARG   0.005   0.000   ARG B 197 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8108.03 seconds
wall clock time: 142 minutes 23.49 seconds (8543.49 seconds total)